So after long calls with Intuit tax expert, who said yes it is a bug and a technical department who told me that they don't know and I should talk to their tax expert or even better upgrade their solution to even more expensive one I decided to go with H &R Block which calculated the taxes properly.

I have verified this appears to ignore anything in line. L-9 and in fact is using the summary deduction on the Quebec portion from the T-4 and not from the Releve -1.   This is clearly an issue and for anyone getting any stock options it is a serious miscalculation.   

Turbotax support called me admitting this is a bug, they are working on the fix, no timeline yet.

Still not fixed by intuit, probably start looking for another solution at this moment

Looks like intuit decided to not care about this bug and not fix it. 

Use other software to do your taxes.